Gosh, I connected to this song immediately, and I'm going to post about it again today because I had an epiphany while driving today. First off, I'll apologize if someone else already said this because I haven't read through this topic in a bit. It is also very close to what I have written before but today something struck me as slightly differnt and I had to share.
The meaning I get from this song is a crisis of faith. But not just faith of religion; faith in love, faith in life, faith in creativity, faith for faith's sake and of course faith in the spiritual and religious senses. I remember her saying this was the first song she wrote in a long time, it was what broke her writer's block. I think it is because it expresses all the crisis of faith that she was feeling in herself, in others, and in the world around her. She was finally able to express all the "crisis" she was feeling. "looking for the secrets" is looking for all the answers to every question that crisis in faith brings about. She was searching for meaning and searching for reasons.
That is what it means to me, and even if that's not what it means to her, it will always strike me in this way.